the alternative you propose is that everyone writes code that only targets well-supported javascript, but does that exclude polyfills or convenience functions? Does that mean that using a polyfill for Array.prototype.map is worse than using an implementation like _.map or a hand-written map function? At best, this choice results in a complex maintenance burden that is borne by developers during future refactors (rather than an infra-focused developer upgrading the babel distribution and its presets/plugins)
the current reality is that the browser ecosystem remains heterogenous (which is why there is still a valid market for things like jquery). A plugin like babel-preset-env for instance allows you to dynamically adjust the "minimum requirements" without needing to write new polyfills and gives the benefit of improving the transformed code with little to developer intervention. It's computers doing what they're good at, i struggle to see the harm in that.